Background Studies demonstrated the bond strength enhancement and the decrease in degradation of the adhesive interface after applying either self-etch adhesives or two-step, etch-and-rinse adhesives under an electric field. However, the presence of dentinal fluid driven by the pulpal pressure in vivo is a profounding factor affecting both the sealing ability and bond strength of adhesives. This study aimed to evaluate the effect of three-step etch-and-rinse and two-step self-etch adhesives when applied with iontophoresis under simulated pulpal pressure on the permeability of dentin, resin infiltration, and the sealing ability of resin composite. Methods The experiments were done on 32 recently extracted premolars, randomly assigned into four groups (n = 8) according to two adhesive systems (SBMP and SE), applied following the manufacturer’s instructions (control) for two groups or with iontophoresis for the others (SBMPi and SEi). For the iontophoresis, the anodal current was applied at 75 μA for 20 s through the cavity electrode during the bond. The fluid flow rate of dentin was recorded after cavity preparation (smear-layer-covered dentin; T1), bonding (T2), and composite restoration (T3) during the maintained pulpal pressure of 20 mm Hg. The flow rates were expressed as a percentage relative to the initial smear-layer-covered value for each specimen. Results were analyzed using repeated measures ANOVA. Scanning electron microscopy (SEM) was performed to observe the resin/dentin interface. Results There were no significant increases in the mean flow rates from T1 to T3 in the SBMP (P = 0.355), while these changes in the SE were significant between T1 (100%) and T2 (166.77%) and T1 and T3 (221.16%) (P = 0.002; one-way RM ANOVA; Holm-Sidak test). For the iontophoresis groups, the mean flow rates decreased significantly from T1 to T2 and T1 to T3 of both SBMPi (T2 = 86.43, and T3 = 79.53; P < 0.001) and SEi groups (T2 = 87.96, and T3 = 81.48; P = 0.004). The iontophoresis of both adhesives produced the optimal resin infiltration with improved quality of the hybrid layer and resin tags. Conclusions SBMP bonded with or without iontophoresis performed better sealing ability than SE under the same condition. Both adhesives applied with anodal iontophoresis significantly decreased the dentin permeability, contributing to the improved resin infiltration.